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Introduction: Several nations around the world had to close schools, colleges, universities, and other educational institutions as they were badly affected by the spread of COVID-19. The purpose of this study was to measure the effectiveness of online vs physical teaching during the COVID-19 pandemic, at the Faculty of Allied Health Sciences (FAHS), University of Ruhuna (UoR) Sri Lanka. Method: A cross-sectional study was conducted among 200 undergraduates. The data were collected through displayed/approved results sheets of the students of selected batches in the Department of Nursing, Department of Pharmacy, and Medical Laboratory Science (MLS). Paired sample T-test was used to compare the results of undergraduates. Results: The examination results of 47-54 undergraduates in nursing, 28 in pharmacy, and 22 in MLS were analysed. Significant differences in Psychiatry in Nursing and Nursing Clinical Attachment were identified in the Department of Nursing (p=0.001). In the Department of Pharmacy, only Pharmaceutical Chemistry I (p=0.012) reported a significant difference. The undergraduates of MLS who underwent online theory sessions had scored more in Microbiology and Immunology (p=0.022) and Basic Genetics and Molecular Biology (p=0.000) whereas in Research Methodology and Epidemiology, the undergraduates who participated in physical lectures had scored more marks (p=0.001). Conclusion: Practical/interactive session-based course units and clinical appointments had a higher impact on the mode of teaching than many theoretical course units. The results might serve as a primer for the creation of an action plan to support the academics and clinical/practical components of undergraduates. [ABSTRACT FROM AUTHOR]